A candidate RNAi screen reveals diverse RNA-binding protein phenotypes in Drosophila flight muscle
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ABSTRACT:
PROVIDER: PRJNA762688 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR15861966_1.fastq.gz | Fastqsanger.gz | |||
| SRR15861966_2.fastq.gz | Fastqsanger.gz | |||
| SRR15861967_1.fastq.gz | Fastqsanger.gz | |||
| SRR15861967_2.fastq.gz | Fastqsanger.gz | |||
| SRR15861968_1.fastq.gz | Fastqsanger.gz |
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Project description:The proper regulation of RNA processing is critical for muscle development and the fine-tuning of contractile ability among muscle fiber-types. RNA binding proteins (RBPs) regulate the diverse steps in RNA processing including alternative splicing, which generates fiber-type specific isoforms of structural proteins that confer contractile sarcomeres with distinct biomechanical properties. Alternative splicing is disrupted in muscle diseases such as myotonic dystrophy and dilated cardiomyopathy, and is altered after intense exercise as well as with aging. It is therefore important to understand splicing and RBP function, but currently only a small fraction of the hundreds of annotated RBPs expressed in muscle have been characterized. Here we demonstrate the utility of Drosophila as a genetic model system to investigate basic developmental mechanisms of RBP function in myogenesis. We find that RBPs exhibit dynamic temporal and fiber-type specific expression patterns in mRNA-Seq data and display muscle-specific phenotypes. We performed knockdown with 105 RNAi hairpins targeting 35 RBPs and report associated lethality, flight, myofiber and sarcomere defects, including flight muscle phenotypes for Doa, Rm62, mub, mbl, sbr, and clu. Interestingly, knockdown phenotypes of spliceosome components, as highlighted by phenotypes for A-complex components SF1 and Hrb87F (hnRNPA1), revealed level- and temporal-dependent myofibril defects. We further show that splicing mediated by SF1 and Hrb87F is necessary for Z-disc stability and proper myofibril development, and strong knockdown of either gene results in impaired localization of Kettin to the Z-disc. Our results expand the number of RBPs with a described phenotype in muscle and underscore the diversity in myofibril and transcriptomic phenotypes associated with splicing defects. Drosophila is thus a powerful model to gain disease-relevant insight into cellular and molecular phenotypes observed when expression levels of splicing factors, spliceosome components and splicing dynamics are altered.
2021-09-15 | GSE184001 | GEO
Project description:The proper regulation of RNA processing is critical for muscle development and the fine-tuning of contractile ability among muscle fiber-types. RNA binding proteins (RBPs) regulate the diverse steps in RNA processing, including alternative splicing, which generates fiber-type specific isoforms of structural proteins that confer contractile sarcomeres with distinct biomechanical properties. Alternative splicing is disrupted in muscle diseases such as myotonic dystrophy and dilated cardiomyopathy and is altered after intense exercise as well as with aging. It is therefore important to understand splicing and RBP function, but currently, only a small fraction of the hundreds of annotated RBPs expressed in muscle have been characterized. Here, we demonstrate the utility of Drosophila as a genetic model system to investigate basic developmental mechanisms of RBP function in myogenesis. We find that RBPs exhibit dynamic temporal and fiber-type specific expression patterns in mRNA-Seq data and display muscle-specific phenotypes. We performed knockdown with 105 RNAi hairpins targeting 35 RBPs and report associated lethality, flight, myofiber and sarcomere defects, including flight muscle phenotypes for Doa, Rm62, mub, mbl, sbr, and clu. Knockdown phenotypes of spliceosome components, as highlighted by phenotypes for A-complex components SF1 and Hrb87F (hnRNPA1), revealed level- and temporal-dependent myofibril defects. We further show that splicing mediated by SF1 and Hrb87F is necessary for Z-disc stability and proper myofibril development, and strong knockdown of either gene results in impaired localization of kettin to the Z-disc. Our results expand the number of RBPs with a described phenotype in muscle and underscore the diversity in myofibril and transcriptomic phenotypes associated with splicing defects. Drosophila is thus a powerful model to gain disease-relevant insight into cellular and molecular phenotypes observed when expression levels of splicing factors, spliceosome components and splicing dynamics are altered.
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Project description:M1BP RNAi during Drosophila flight myogenesis: Analyses at 0h APF stage
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Project description:M1BP RNAi during Drosophila flight myogenesis: Analyses at 48h APF stage
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Project description:M1BP RNAi during Drosophila flight myogenesis: Analyses at 64h APF stage
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Project description:M1BP RNAi during Drosophila flight myogenesis: Analyses at 2-day adult stage
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Project description:RNA-seq to analyse differential expression between moths (Helicoverpa armigera) flown on tethered flight mills. Insects were split into two phenotypes based on the distance flown during the course of a single night. Two separate comparisons were performed. The first compared long-distance fliers from Dafeng (DF) with short-distance fliers from Anyang (AY). These are two separate populations approximately 650km apart in China. The second comparison looked at two flight phenotypes from the same population originating from Northern Greece (GR).
2015-08-31 | E-MTAB-3790 | biostudies-arrayexpress
Project description:In Drosophila, fibrillar flight muscles (IFMs) enable flight, while tubular muscles mediate other body movements. Here, we use RNA-sequencing and isoform-specific reporters to show that spalt major (salm) determines fibrillar muscle physiology by regulating transcription and alternative splicing of a large set of sarcomeric proteins. We identify the RNA binding protein Arrest (Aret, Bruno) as downstream of salm. Aret shuttles between cytoplasm and nuclei, and is essential for myofibril maturation and sarcomere growth of IFMs. Molecularly, Aret regulates IFM-specific transcription and splicing of various sarcomeric targets, including Stretchin and wupA (TnI), and thus maintains muscle fiber integrity. As Aret and its sarcomeric targets are evolutionarily conserved, similar principles may regulate mammalian muscle morphogenesis. 9 samples from Drosophila melanogaster were analyzed in duplicate: control dissected wildtype flight muscle at 30h APF, 72h APF and 0 day adult, jump muscle and whole leg from 1d adult and RNAi/mutant conditions for salm (1d flight muscle) and aret (30h, 72h and 1d flight muscle)
2014-12-23 | E-GEOD-63707 | biostudies-arrayexpress
Project description:Muscle development and diversity require a large number of spatially and temporally regulated events controlled by transcription factors (TFs). Drosophila has long stood as a model organism to study myogenesis due to the highly conserved key TFs involved at all stages of muscle development, from specification to differentiation. While many studies focused on the diversification of Drosophila larval musculature, how distinct adult muscle types are generated is much less characterised. Here, we identify a novel essential regulator of Drosophila thoracic flight muscle development, the Hox TF Antennapedia (Antp). Correcting a long standing misconception that flight muscle development occurs without the input of Hox TFs, we show that Antp intervenes at several stages of adult flight muscle development, from the establishment of the progenitor pool in the embryo to myoblast differentiation in the early pupa. Furthermore, the precisely regulated clearance of Hox at the pupal stage in the developing indirect flight muscle fibers is required to allow for stretch-activated fibrillar muscle fate diversification that sets these flight muscles apart from all other adult tubular muscle types.
2024-10-23 | GSE268578 | GEO
Project description:Honey bees move through a series of in-hive tasks (M-bM-^@M-^\nursingM-bM-^@M-^]) to outside tasks (M-bM-^@M-^\foragingM-bM-^@M-^]) that coincident with an intense increase in metabolic activity. Social context can cause worker bees to speed up, or slow down this process and foragers may revert back to their earlier in hive tasks accompanied by reversion to earlier physiological states. To determine if the transcriptional profile of forager bees can revert, or if the effects of flight on gene expression are irreversible, we used whole-genome microarrays. Brain tissue and flight muscle exhibited independent patterns of expression during behavioral transitions, with patterns of expression in the brain reflecting both age and behavior, while flight muscle exhibited primarily age-related patterns of expression. Our data suggest that the transition from little to no flight (nurse) to intense flight (forager), rather than the amount of flight has a major effect on gene expression. Following behavioral reversion there was a partial reversion in gene expression but some aspects of forager expression patterns, such as those for genes involved in immune function, remained. These data suggest an epigenetic control and energy balance role in honey bee functional senescence. Brains and thoraces from the same individuals of all behavioral groups were compared on a total of 132 arrays. The samples were hybridized against each other using a loop design. The groups tested are outlined as follows: Typical aged nurse 'YN' (8-10 days old; <1 day flight experience), Precocious forager 'PF' (8 to 10 days old; 2 to 3 days flight experience), Overaged nurse 'ON' (19 to 22 days old; < 1 day flight experience), Forager - low flight 'TFL' (19 to 22 days old; 2 to 3 days flight experience), Forager - high flight 'TFH' ( 19 to 22 days old; 7 to 9 days flight experience), Forager - old 'OF' (25 to 26 days old; 10 to 12 days flight experience), Reverted nurse 'RN' (25 to 26 days old; 7 to 9 days flight experience). The comparisons are outlined as follows: YN:ON (6 arrays), ON:RN (6 arrays), RN:TFH (6 arrays), TFH:TFL (6 arrays), TFL:PF (6 arrays), PF:YN (6 arrays), ON:TFL (12 arrays), YN:OF (6 arrays), OF:RN (6 arrays), RN:YN (6 arrays). Each comparison was done for individual brains and thoraces. Total: 132 arrays
2012-10-01 | E-GEOD-40650 | biostudies-arrayexpress